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One needs acoustic signals for underwater communication. I work with underwater modems, and we use frequencies in the 18-34 KHz range. Other modems can operate in bands from 8-50 KHz.

Autonomous underwater vehicles are an active area of research. One of the challenges involved are localization once the vehicle has dived. You cannot get GPS under water, so one way to localize yourself is by tracking your velocity/acceleration once the dive has begun. Another way is to exchange messages with your peer robots and devise a distributed location resolution scheme. See some of the work done in my lab in these areas: http://arl.nus.edu.sg/twiki/bin/view/ARL/STARFISH